A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
This report has been generated by the nf-core/sarek analysis pipeline. For information about how to interpret these results, please see the documentation.
Report
generated on 2025-07-11, 12:43 CEST
based on data in:
/home/dolmom/Desktop/cnv_pipeline/work/12/939494e50a083f6d02898d7944d9b1
General Statistics
| Sample Name | Vars | SNP | Indel | Ts/Tv | MNP | Multiallelic | Multiallelic SNP |
|---|---|---|---|---|---|---|---|
| test_sample.manta.diploid_sv | 10306 | 0 | 5395 | 0.00 | 1 | 0 | 0 |
Bcftools
Utilities for variant calling and manipulating VCFs and BCFs.URL: https://samtools.github.io/bcftoolsDOI: 10.1093/gigascience/giab008
Variant Substitution Types
Variant Quality
Indel Distribution
Vcftools
Program to analyse and reporting on VCF files.URL: https://vcftools.github.ioDOI: 10.1093/bioinformatics/btr330
TsTv by Count
Plot of TSTV-BY-COUNT - the transition to transversion ratio as a function of alternative allele count from the output of vcftools TsTv-by-count.
Transition is a purine-to-purine or pyrimidine-to-pyrimidine point mutations.
Transversion is a purine-to-pyrimidine or pyrimidine-to-purine point mutation.
Alternative allele count is the number of alternative alleles at the site.
Note: only bi-allelic SNPs are used (multi-allelic sites and INDELs are skipped.)
Refer to Vcftools's manual (https://vcftools.github.io/man_latest.html) on --TsTv-by-count
TsTv by Qual
Plot of TSTV-BY-QUAL - the transition to transversion ratio as a function of SNP quality from the output of vcftools TsTv-by-qual.
Transition is a purine-to-purine or pyrimidine-to-pyrimidine point mutations.
Transversion is a purine-to-pyrimidine or pyrimidine-to-purine point mutation.
Quality here is the Phred-scaled quality score as given in the QUAL column of VCF.
Note: only bi-allelic SNPs are used (multi-allelic sites and INDELs are skipped.)
Refer to Vcftools's manual (https://vcftools.github.io/man_latest.html) on --TsTv-by-qual
Software Versions
Software Versions lists versions of software tools extracted from file contents.
| Group | Software | Version |
|---|---|---|
| BCFTOOLS_STATS | bcftools | 1.2 |
| MANTA_GERMLINE | manta | 1.6.0 |
| VCFTOOLS_TSTV_COUNT | vcftools | 0.1.16 |
| Workflow | Nextflow | 25.04.6 |
| nf-core/sarek | v3.5.1-g5fe5cdf |
nf-core/sarek Methods Description
Suggested text and references to use when describing pipeline usage within the methods section of a publication.URL: https://github.com/nf-core/sarek
Methods
Data was processed using nf-core/sarek v3.5.1 (doi: 10.12688/f1000research.16665.2), (doi: 10.1093/nargab/lqae031), (doi: 10.5281/zenodo.3476425) of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.
The pipeline was executed with Nextflow v25.04.6 (Di Tommaso et al., 2017) with the following command:
nextflow run nf-core/sarek -profile singularity -params-file params_PGP.yml
References
- Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
- Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
- Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
- da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192
Notes:
- The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
- You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.
nf-core/sarek Workflow Summary
- this information is collected when the pipeline is started.URL: https://github.com/nf-core/sarek
Input/output options
- input
- input/sample.csv
- outdir
- results/
- step
- variant_calling
Main options
- intervals
- s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/intervals/wgs_calling_regions_noseconds.hg38.bed
- tools
- manta
Variant Calling
- cf_chrom_len
- s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/Length/Homo_sapiens_assembly38.len
- pon
- s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz
- pon_tbi
- s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz.tbi
Reference genome options
- ascat_alleles
- s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/G1000_alleles_hg38.zip
- ascat_genome
- hg38
- ascat_loci
- s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/G1000_loci_hg38.zip
- ascat_loci_gc
- s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/GC_G1000_hg38.zip
- ascat_loci_rt
- s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/RT_G1000_hg38.zip
- bwa
- s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/BWAIndex/
- bwamem2
- s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/BWAmem2Index/
- chr_dir
- s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/Chromosomes
- dbsnp
- s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz
- dbsnp_tbi
- s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi
- dbsnp_vqsr
- --resource:dbsnp,known=false,training=true,truth=false,prior=2.0 dbsnp_146.hg38.vcf.gz
- dict
- s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict
- dragmap
- s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/dragmap/
- fasta
- s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
- fasta_fai
- s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai
- germline_resource
- s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz
- germline_resource_tbi
- s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz.tbi
- known_indels
- s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz
- known_indels_tbi
- s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi
- known_indels_vqsr
- --resource:gatk,known=false,training=true,truth=true,prior=10.0 Homo_sapiens_assembly38.known_indels.vcf.gz --resource:mills,known=false,training=true,truth=true,prior=10.0 Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
- known_snps
- s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000G_omni2.5.hg38.vcf.gz
- known_snps_tbi
- s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000G_omni2.5.hg38.vcf.gz.tbi
- known_snps_vqsr
- --resource:1000G,known=false,training=true,truth=true,prior=10.0 1000G_omni2.5.hg38.vcf.gz
- mappability
- s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/Control-FREEC/out100m2_hg38.gem
- ngscheckmate_bed
- s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/NGSCheckMate/SNP_GRCh38_hg38_wChr.bed
- sentieon_dnascope_model
- s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/Sentieon/SentieonDNAscopeModel1.1.model
- snpeff_db
- GRCh38.105
- vep_cache_version
- 113
- vep_genome
- GRCh38
- vep_species
- homo_sapiens
Core Nextflow options
- configFiles
- /home/dolmom/.nextflow/assets/nf-core/sarek/nextflow.config
- containerEngine
- singularity
- launchDir
- /home/dolmom/Desktop/cnv_pipeline
- profile
- singularity
- projectDir
- /home/dolmom/.nextflow/assets/nf-core/sarek
- revision
- master
- runName
- prickly_raman
- userName
- dolmom
- workDir
- /home/dolmom/Desktop/cnv_pipeline/work